# Analysis of Large-Scale Toxico-Genomic Data

## Documentation for package ‘ToxicoGx’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D F H L M N P S T U misc

## -- A --

annotation | Accessing and modifying information in a 'CoreSet'
annotation-method | Accessing and modifying information in a 'CoreSet'
annotation<- | Accessing and modifying information in a 'CoreSet'
annotation<--method | Accessing and modifying information in a 'CoreSet'
availableTSets | Return a table of ToxicoSets available for download

## -- C --

cellInfo | Accessing and modifying information in a 'CoreSet'
cellInfo-method | Accessing and modifying information in a 'CoreSet'
cellInfo<- | Accessing and modifying information in a 'CoreSet'
cellInfo<--method | Accessing and modifying information in a 'CoreSet'
cellName-method | Accessing and modifying information in a 'CoreSet'
cellNames | Accessing and modifying information in a 'CoreSet'
cellNames<- | Accessing and modifying information in a 'CoreSet'
cellNames<--method | Accessing and modifying information in a 'CoreSet'
checkTSetStructure | A function to verify the structure of a ToxicoSet
computeAUC | Computes the AUC for a Drug Dose Viability Curve
computeIC50 | Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve
computeICn | Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve
computeLimmaDiffExpr | Generic method for performing differential expression analysis on an S4 object using the limma package
computeLimmaDiffExpr-method | Conduct differential expression analysis using the limma R pacakge
curation | Accessing and modifying information in a 'CoreSet'
curation-method | Accessing and modifying information in a 'CoreSet'
curation<- | Accessing and modifying information in a 'CoreSet'
curation<--method | Accessing and modifying information in a 'CoreSet'

## -- D --

datasetType | Accessing and modifying information in a 'CoreSet'
datasetType-method | Accessing and modifying information in a 'CoreSet'
datasetType<- | Accessing and modifying information in a 'CoreSet'
datasetType<--method | Accessing and modifying information in a 'CoreSet'
dateCreated | Accessing and modifying information in a 'CoreSet'
dateCreated-method | Accessing and modifying information in a 'CoreSet'
dateCreated<- | Accessing and modifying information in a 'CoreSet'
dateCreated<--method | Accessing and modifying information in a 'CoreSet'
dim-method | Get the dimensions of a ToxicoSet
downloadTSet | Download a ToxicoSet object
drugGeneResponseCurve | Compares gene expression for a specificed set of features over specific drug dosages vs time
drugInfo | Accessing and modifying information in a 'CoreSet'
drugInfo<- | Accessing and modifying information in a 'CoreSet'
drugNames | Accessing and modifying information in a 'CoreSet'
drugNames<- | Accessing and modifying information in a 'CoreSet'
drugPerturbationSig | Drug perturbation analysis
drugTimeResponseCurve | Compares viabilities at a given dose over different experimental durations

## -- F --

featureInfo | Accessing and modifying information in a 'CoreSet'
featureInfo-method | Accessing and modifying information in a 'CoreSet'
featureInfo<- | Accessing and modifying information in a 'CoreSet'
featureInfo<--method | Accessing and modifying information in a 'CoreSet'
fNames | Accessing and modifying information in a 'CoreSet'
fNames-method | Accessing and modifying information in a 'CoreSet'
fNames<- | Accessing and modifying information in a 'CoreSet'
fNames<--method | Accessing and modifying information in a 'CoreSet'

## -- H --

HCC_sig | HCC_sig dataset

## -- L --

logLogisticRegression | Fits curves of the form E = E_inf + (1 - E_inf)/(1 + (c/EC50)^HS) to dose-response data points (c, E) given by the user and returns a vector containing estimates for HS, E_inf, and EC50.

## -- M --

mDataNames | Accessing and modifying information in a 'CoreSet'
mDataNames-method | Accessing and modifying information in a 'CoreSet'
mDataNames<- | Accessing and modifying information in a 'CoreSet'
mDataNames<--method | Accessing and modifying information in a 'CoreSet'
molecularProfiles | Accessing and modifying information in a 'CoreSet'
molecularProfiles-method | Accessing and modifying information in a 'CoreSet'
molecularProfiles<- | Accessing and modifying information in a 'CoreSet'
molecularProfiles<--method | Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot | Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot-method | Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot<- | Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot<--method | Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot<-ToxicoSet-method | Accessing and modifying information in a 'CoreSet'
moleculerProfilesSlot-method | Accessing and modifying information in a 'CoreSet'

## -- N --

name | Accessing and modifying information in a 'CoreSet'
name-method | Accessing and modifying information in a 'CoreSet'
name<- | Accessing and modifying information in a 'CoreSet'
name<--method | Accessing and modifying information in a 'CoreSet'

## -- P --

pertNumber | Accessing and modifying information in a 'CoreSet'
pertNumber-method | Accessing and modifying information in a 'CoreSet'
pertNumber<- | Accessing and modifying information in a 'CoreSet'
pertNumber<--method | Accessing and modifying information in a 'CoreSet'
phenoInfo | Accessing and modifying information in a 'CoreSet'
phenoInfo-method | Accessing and modifying information in a 'CoreSet'
phenoInfo<- | Accessing and modifying information in a 'CoreSet'
phenoInfo<--method | Accessing and modifying information in a 'CoreSet'

## -- S --

sampleInfo | Accessing and modifying information in a 'CoreSet'
sampleInfo-method | Accessing and modifying information in a 'CoreSet'
sampleInfo<- | Accessing and modifying information in a 'CoreSet'
sampleInfo<--method | Accessing and modifying information in a 'CoreSet'
sampleName-method | Accessing and modifying information in a 'CoreSet'
sampleNames | Accessing and modifying information in a 'CoreSet'
sampleNames-method | Accessing and modifying information in a 'CoreSet'
sampleNames<- | Accessing and modifying information in a 'CoreSet'
sampleNames<--method | Accessing and modifying information in a 'CoreSet'
sensitivityInfo-method | Accessing and modifying information in a 'CoreSet'
sensitivityInfo<--method | Accessing and modifying information in a 'CoreSet'
sensitivityMeasures-method | Accessing and modifying information in a 'CoreSet'
sensitivityMeasures<--method | Accessing and modifying information in a 'CoreSet'
sensitivityProfiles-method | Accessing and modifying information in a 'CoreSet'
sensitivityProfiles<--method | Accessing and modifying information in a 'CoreSet'
sensitivityRaw-method | Accessing and modifying information in a 'CoreSet'
sensitivityRaw<--method | Accessing and modifying information in a 'CoreSet'
sensitivitySlot | Accessing and modifying information in a 'CoreSet'
sensitivitySlot-method | Accessing and modifying information in a 'CoreSet'
sensitivitySlot<- | Accessing and modifying information in a 'CoreSet'
sensitivitySlot<--method | Accessing and modifying information in a 'CoreSet'
sensitvityInfo<--method | Accessing and modifying information in a 'CoreSet'
sensNumber | Accessing and modifying information in a 'CoreSet'
sensNumber-method | Accessing and modifying information in a 'CoreSet'
sensNumber<- | Accessing and modifying information in a 'CoreSet'
sensNumber<--method | Accessing and modifying information in a 'CoreSet'
show-method | Show a ToxicoSet
show-method | Show ToxicoGx Signatures
showSigAnnot | Show the Annotations of a signature object
subsetTo | A function to subset a ToxicoSet to data containing only specified drugs, cells and genes
summarizeMolecularProfiles | Takes molecular data from a ToxicoSet, and summarises them into one entry per drug and experimental condition.
summarizeSensitivityProfiles | Takes the sensitivity data from a ToxicoSet, and summarises them into a drug vs cell line table

## -- T --

TGGATESsmall | TGGATESsmall dataset
ToxicoSet | ToxicoSet constructor
ToxicoSet-accessors | Accessing and modifying information in a 'CoreSet'
ToxicoSet-class | Class to contain Toxico-genomic Data
treatmentInfo | Accessing and modifying information in a 'CoreSet'
treatmentInfo-method | Accessing and modifying information in a 'CoreSet'
treatmentInfo<- | Accessing and modifying information in a 'CoreSet'
treatmentInfo<--method | Accessing and modifying information in a 'CoreSet'
treatmentNames | Accessing and modifying information in a 'CoreSet'
treatmentNames-method | Accessing and modifying information in a 'CoreSet'
treatmentNames<- | Accessing and modifying information in a 'CoreSet'
treatmentNames<--method | Accessing and modifying information in a 'CoreSet'

## -- U --

updateObject-method | Update the ToxicoSet class after changes in it struture or API

## -- misc --

.ToxicoSet | Class to contain Toxico-genomic Data
[-method | '['